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- PDB-8gt7: Structure of falcipain and human Stefin A mutant complex -

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Basic information

Entry
Database: PDB / ID: 8gt7
TitleStructure of falcipain and human Stefin A mutant complex
Components
  • Cystatin-A
  • Cysteine proteinase falcipain 2a
  • LYS-GLU-ILE-VAL-ASN-PRO-LEU-THR-LYS
  • VAL-ASN-PRO-LEU-THR-LYS-LYS-GLY-GLU
KeywordsHYDROLASE / falcipain / stefin / complex
Function / homology
Function and homology information


negative regulation of peptidase activity / peptidase inhibitor complex / food vacuole / Formation of the cornified envelope / peptide cross-linking / cornified envelope / cysteine-type endopeptidase inhibitor activity / keratinocyte differentiation / proteolysis involved in protein catabolic process / negative regulation of proteolysis ...negative regulation of peptidase activity / peptidase inhibitor complex / food vacuole / Formation of the cornified envelope / peptide cross-linking / cornified envelope / cysteine-type endopeptidase inhibitor activity / keratinocyte differentiation / proteolysis involved in protein catabolic process / negative regulation of proteolysis / cell-cell adhesion / protease binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cysteine-type endopeptidase activity / proteolysis / extracellular space / nucleoplasm / membrane / cytosol / cytoplasm
Similarity search - Function
Proteinase inhibitor I25A, stefin / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Cystatin superfamily / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) ...Proteinase inhibitor I25A, stefin / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Cystatin superfamily / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / DI(HYDROXYETHYL)ETHER / Cystatin-A / Falcipain-2a
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 Å
AuthorsChakraborty, S. / Biswas, S.
Funding support India, 1items
OrganizationGrant numberCountry
Other government India
CitationJournal: To Be Published
Title: Structure of falcipain and human Stefin A complex
Authors: Chakraborty, S. / Biswas, S.
History
DepositionSep 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine proteinase falcipain 2a
B: Cystatin-A
C: Cysteine proteinase falcipain 2a
D: Cystatin-A
E: LYS-GLU-ILE-VAL-ASN-PRO-LEU-THR-LYS
F: VAL-ASN-PRO-LEU-THR-LYS-LYS-GLY-GLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,012242
Polymers78,5396
Non-polymers27,473236
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.461, 119.620, 65.016
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Cysteine proteinase falcipain 2a /


Mass: 27205.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: PF3D7_1115700 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8I6U4, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein Cystatin-A / Cystatin-AS / Stefin-A


Mass: 11048.478 Da / Num. of mol.: 2 / Mutation: K68R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSTA, STF1, STFA / Production host: Escherichia coli (E. coli) / References: UniProt: P01040

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Protein/peptide , 2 types, 2 molecules EF

#3: Protein/peptide LYS-GLU-ILE-VAL-ASN-PRO-LEU-THR-LYS


Mass: 1043.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Production host: Escherichia coli (E. coli)
#4: Protein/peptide VAL-ASN-PRO-LEU-THR-LYS-LYS-GLY-GLU


Mass: 987.151 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Production host: Escherichia coli (E. coli)

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Non-polymers , 8 types, 431 molecules

#5: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 65 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: Na
#7: Chemical...
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#8: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#9: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 54 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Polyethylene glycol


Mass: 370.436 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C16H34O9 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.06 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 0.05 M cadmium chloride, 0.1 M Na HEPES pH 7.5 and 1.5 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 3.28→44.02 Å / Num. obs: 14680 / % possible obs: 99.74 % / Redundancy: 6.2 % / Biso Wilson estimate: 88.6 Å2 / Rmerge(I) obs: 0.311 / Net I/σ(I): 4.7
Reflection shellResolution: 3.28→3.4 Å / Num. unique obs: 1447 / CC1/2: 0.368

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.28→42.09 Å / SU ML: 0.4925 / Cross valid method: FREE R-VALUE / σ(F): 0.11 / Phase error: 29.9907
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2997 715 10 %
Rwork0.2717 24438 -
obs0.2745 14680 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.23 Å2
Refinement stepCycle: LAST / Resolution: 3.28→42.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5514 0 1794 195 7503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00687187
X-RAY DIFFRACTIONf_angle_d1.32049043
X-RAY DIFFRACTIONf_chiral_restr0.0695807
X-RAY DIFFRACTIONf_plane_restr0.0096996
X-RAY DIFFRACTIONf_dihedral_angle_d28.72763012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.28-3.340.3481520.27471252X-RAY DIFFRACTION99.93
3.34-3.40.2951530.26621333X-RAY DIFFRACTION99.87
3.4-3.470.2821420.25491287X-RAY DIFFRACTION99.93
3.47-3.550.28681510.25161266X-RAY DIFFRACTION99.86
3.55-3.630.26891420.26081293X-RAY DIFFRACTION99.93
3.63-3.720.36291340.26261268X-RAY DIFFRACTION99.64
3.72-3.820.32451590.27361331X-RAY DIFFRACTION99.73
3.82-3.930.37581400.24621276X-RAY DIFFRACTION99.65
3.94-4.060.26631420.26621273X-RAY DIFFRACTION99.51
4.06-4.210.31361460.24091280X-RAY DIFFRACTION98.34
4.21-4.380.30251350.23961247X-RAY DIFFRACTION95.64
4.38-4.570.3191430.23661274X-RAY DIFFRACTION99.44
4.57-4.810.25291410.2461288X-RAY DIFFRACTION99.72
4.82-5.120.27711410.26741301X-RAY DIFFRACTION99.93
5.12-5.510.27211390.27431289X-RAY DIFFRACTION99.72
5.51-6.060.3091440.30261304X-RAY DIFFRACTION99.93
6.06-6.940.351390.33921288X-RAY DIFFRACTION99.58
6.94-8.720.27471330.28151294X-RAY DIFFRACTION99.72
8.73-42.090.29941400.29641294X-RAY DIFFRACTION98.62

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